Item Details

abstract

Ribosome frameshifting, pausing, and termination events have a profound effect on the accuracy and reliability of protein synthesis. A variety of translational control mechanisms combine to ensure the fidelity of this process. Mechanisms, such as aminoacyl-tRNA selection and codon:anticodon interactions, are well characterized. However, more complex mechanisms, such as mRNA secondary structures, require a new approach for further study. We suggest that these mechanisms may be studied on a global scale by mapping the distribution of ribosomes along a select group of mRNAs. A combination of techniques for ribosome-protected mRNA fragment isolation (ribosome footprinting) and high-throughput sequencing—a method for simultaneously sequencing up to 40 million fragments—provides the tools for studying global translational control mechanisms. We plan to sequence a set of ribosome footprints using Illumina’s Genome Analyzer, which requires the presence of two unique adapter sequences on either end of these fragments. Conventional methods for adding these adapter sequences to RNA fragments result in significant material loss. Here we propose an improved method for isolating and converting small RNA fragments to a sequencing-ready form without the use of gel purification or sample amplification (PCR) steps. We also critique a similar method published by Ingolia, et al., (2009).

subject

Translation

Protein Synthesis

Ribosomes

High-throughput Sequencing

contributor

Bender, R. Hugh F. (author)

Tague, Brian (committee chair)

Curran, James (committee member)

Fetrow, Jacquelyn (committee member)

Ornelles, David (committee member)

date

2009-08-03T14:30:12Z (accessioned)

2010-06-18T18:59:28Z (accessioned)

2009-08-03T14:30:12Z (available)

2010-06-18T18:59:28Z (available)

2009-08-03T14:30:12Z (issued)

degree

Biology (discipline)

identifier

http://hdl.handle.net/10339/14857 (uri)

language

en_US (iso)

publisher

Wake Forest University

rights

Release the entire work for access only to the Wake Forest University system for one year from the date below. After one year, release the entire work for access worldwide. (accessRights)

title

A METHOD FOR IDENTIFYING RIBOSOME PAUSE SITES IN MESSENGER RNA THROUGH NEW SEQUENCING TECHNOLOGY

type

Thesis